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Expression data in Arabidopsis fry1-6, xrn2-4, xrn3-3 and xrn4-6 mutants.

ABSTRACT: We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis fry1-6, xrn2-4, xrn3-3 and xrn4-6 mutants.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE32977 | GEO | 2012/05/03

SECONDARY ACCESSION(S): PRJNA146425

REPOSITORIES: GEO

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Expression data in Arabidopsis fry1-6, xrn2-4, xrn3-3 and xrn4-6 mutants.

Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis fry1-6, xrn2-4, xrn3-3 and xrn4-6 mutants. The total RNA was prepared from 15-day-old Arabidopsis plants grown on the agar plates and used for the microarray hybridization. Three replicative hybridization experiments for each strand array were carried out using the independent biological RNA samples.

2012-05-02 | E-GEOD-32977 | biostudies-arrayexpress

Arabidopsis mRNA decay landscape shaped by XRN 5′-3′ exoribonucleases

Project description:XRN 5′-3′ exoribonucleases play crucial roles in the control of RNA processing, quality, and quantity in eukaryotes. Although genome-wide profiling of RNA decay fragments is now feasible, how XRNs shape the plant mRNA degradome remains elusive. Here, we profiled and analyzed the RNA degradomes of the Arabidopsis wild type and mutants with defects in XRN activity. Deficiency of nuclear XRN3 or cytoplasmic XRN4 but not nuclear XRN2 activity largely altered Arabidopsis mRNA decay profiles. In addition to the primary XRN4 substrates derived from decapping and microRNA-directed slicing, terminating ribosome- and exon junction complex-protected fragments produced from XRN4-mediated cytoplasmic decay also represent the most abundant decay intermediates of Arabidopsis mRNAs. Short excised linear introns and cleaved pre-mRNA fragments downstream of polyadenylation sites were polyadenylated and stabilized in the xrn3 mutant, demonstrating the function of XRN3 in the removal of cleavage remnants from pre-mRNA processing. Further analysis of stabilized XRN3 substrates confirmed that polyadenylation cleavage frequently occurs after an adenosine. An increase in decay intermediates with 5′ ends upstream of a consensus motif in the xrn4 mutant suggests an endonucleolytic cleavage mechanism targeting the 3′ untranslated region of many Arabidopsis mRNAs. However, analysis of decay fragments stabilized in the xrn4 mutant indicated that, except for microRNA-directed slicing, endonucleolytic cleavage events in the coding sequence might rarely result in major decay intermediates. Together, the results of this study reveal major substrates and products of nuclear and cytoplasmic XRNs along Arabidopsis transcripts and provide a basis for precise interpretation of RNA degradome data.

2022-09-06 | GSE205190 | GEO

Arabidopsis thaliana

Project description:Expression data in Arabidopsis fry1-6, xrn2-4, xrn3-3 and xrn4-6 mutants.

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Genome-wide identification of non-coding RNAs targeted by XRN exoribonucleases in collaboration with FRY1 using RNA-Seq in Arabidopsis thaliana.

Project description:We report new insight of non-coding RNA degradation mediated by XRN exoribonucleases and FRY1 in Arabidopsis thaliana. We suggest that XRN3, in combination with FRY1, is required to prevent the accumulation of 3’ extensions that arise from thousands of mRNA and miRNA precursor transcripts. Examination of genome-wide transcriptomes of Arabidopsis genotypes such as fry1-6, xrn3-3, xrn2-1xrn3-3, xrn2-1xrn4-6 and xrn3-3xrn4-6 using directional RNA-Seq method.

2012-05-02 | E-GEOD-34654 | biostudies-arrayexpress

Expression data in Arabidopsis axe1-5 and met1-3 mutants.

Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis axe1-5 and met1-3 mutants.

2011-05-16 | GSE23950 | GEO

Expression data in Arabidopsis ago1-25 and hyl1-2 mutants.

Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis ago1-25 and hyl1-2 mutants.

2009-12-02 | GSE15699 | GEO

Expression data in Arabidopsis upf1-1 and upf3-1 mutants.

Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis upf1-1 and upf3-1 mutants. Keywords: untreated condition

2009-01-14 | GSE12101 | GEO

Expression data in Arabidopsis rdr2-1 and ddc (drm1-1drm2-2cmt3-11) mutants.

Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis rdr2-1 and ddc mutants. Keywords: untreated condition

2008-10-23 | GSE12549 | GEO

Expression data in Arabidopsis wild type, ahg2-1 and ahg2-1ags1-1 mutants

Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis wild type, ahg2-1 and ahg2-1ags1-1 mutants.

2013-08-09 | GSE46128 | GEO

Defective XRN3-mediated transcription termination in Arabidopsis affects the expression of protein-coding genes [seq]

Project description:Arabidopsis thaliana contains two nuclear XRN2/3 5'-3' exonucleases that are homologs of yeast and human Rat1/Xrn2 proteins involved in the processing and degradation of several classes of nuclear RNAs and in transcription termination of RNA polymerase II. Using strand-specific short read sequencing we show that knockdown of XRN3 leads to an altered expression of hundreds of genes and the accumulation of uncapped and polyadenylated read-through transcripts generated by inefficiently terminated Pol II. Our data support the notion that XRN3-mediated changes in the expression of a subset of genes are caused by upstream read-through transcription and these effects are enhanced by RNA-mRNA chimeras generated in xrn3 plants. In turn, read-through transcripts that are antisense to downstream genes may trigger production of siRNA. Our results highlight the importance of XRN3 exoribonuclease in Pol II transcription termination in plants and show that disturbance in this process may significantly alter gene expression.

2018-01-24 | GSE95473 | GEO

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